In this study, 2D finite element analysis was considered in which the cell was simulated as PHE constitutive material and the cohesive zone formulation was used to define contact between the cell and substrate (see Materials and Model).
Motivated by the assessments of the residue residue contact predictions in Critical Assessment of Protein Structure Prediction (CASP) (Monastyrskyy et al., 2011), NNcon (Tegge et al., 2009) defines contacts between Cβ (Cα for Gly) atoms using two thresholds at 8 and 12 Å; other thresholds are not considered.
The lack of defined contacts between the glucose and the peptide in the sublancin structure do not provide any evidence for a role of the sugar in folding of the peptide as is often seen for glycopeptides, although an interaction with the biosynthetic thiol-disulfide oxidoreductases cannot be ruled out.
The inner (bottom) periplasmic layer was less well visible in the class averages, suggesting a less defined contact between it and the basal body.
A distance cutoff of 6 Å [as used in previous CG studies (46)] was used to define contacts made between the PIP2 headgroup and the Kir channels during the CG simulations.
We use the Euclidean distances between α-carbons to construct a distance matrix D. Using a threshold of 8 Å to define "contact," and excluding trivial contacts (defined as those between residues that are separated by fewer than two intervening residues in the sequence), we convert D to a Boolean contact matrix C, where 1 represents "contact" and 0 represents "no contact".
This work discusses the input parameters of discrete element method (DEM) for defining contact element between concrete and rebar.
Cell surface hydrophobicity was examined using a biophysical assay that defines contact angles between cell surfaces and aqueous solutions (Amaral et al., 2006; Henriques et al., 2007).
Migration modelling based on Fick's law gave a prediction of the Sb migrant concentration under defined contact conditions between food simulant and PET.
Additionally telemetry location estimates are usually too large (within meters) to define probable contacts between small animals like rodents and the costs prohibit marking an entire rodent community.
